diff options
Diffstat (limited to 'pkgs/applications/science')
16 files changed, 61 insertions, 56 deletions
diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix index 34d997252f5..8f60b8b991e 100644 --- a/pkgs/applications/science/biology/kssd/default.nix +++ b/pkgs/applications/science/biology/kssd/default.nix @@ -1,38 +1,57 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, zlib, automake, autoconf, libtool }: +{ lib +, stdenv +, fetchFromGitHub +, fetchpatch +, zlib +, kssd +, runCommand +}: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "kssd"; - version = "1.1"; + version = "2.21"; src = fetchFromGitHub { owner = "yhg926"; repo = "public_kssd"; - rev = "v${version}"; - sha256 = "sha256-8jzYqo9LXF66pQ1EIusm+gba2VbTYpJz2K3NVlA3QxY="; + rev = "v${finalAttrs.version}"; + hash = "sha256-D/s1jL2oKE0rSdRMVljskYFsw5UPOv1L95Of+K+e17w="; }; patches = [ - # Pull upstream patch for -fno-common toolchain support: - # https://github.com/yhg926/public_kssd/pull/9 + # https://github.com/yhg926/public_kssd/pull/11 (fetchpatch { - name = "fno-common.patch"; - url = "https://github.com/yhg926/public_kssd/commit/cdd1e8aae256146f5913a3b4c723b638d53bdf27.patch"; - sha256 = "sha256-HhaTRqPfKR+ouh0PwEH6u22pbuqbX2OypRzw8BXm0W4="; + name = "allocate-enough-memory.patch"; + url = "https://github.com/yhg926/public_kssd/commit/b1e66bbcc04687bc3201301cd742a0b26a87cb5d.patch"; + hash = "sha256-yFyJetpsGKeu+H6Oxrmn5ea4ESVtblb3YJDja4JEAEM="; }) ]; - nativeBuildInputs = [ autoconf automake ]; - buildInputs = [ zlib libtool ]; + buildInputs = [ zlib ]; installPhase = '' - install -vD kssd $out/bin/kssd + runHook preInstall + + install -vD kssd $out/bin/kssd + + runHook postInstall ''; + passthru.tests = { + simple = runCommand "${finalAttrs.pname}-test" { } '' + mkdir $out + ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -r ${kssd.src}/test_fna/seqs1 -o $out/reference + ${lib.getExe kssd} dist -L ${kssd.src}/shuf_file/L3K10.shuf -o $out/query ${kssd.src}/test_fna/seqs2 + ${lib.getExe kssd} dist -r $out/reference -o $out/distout $out/query + ''; + }; + meta = with lib; { description = "K-mer substring space decomposition"; license = licenses.asl20; homepage = "https://github.com/yhg926/public_kssd"; maintainers = with maintainers; [ unode ]; - platforms = [ "x86_64-linux" ]; + platforms = platforms.linux; + mainProgram = "kssd"; }; -} +}) diff --git a/pkgs/applications/science/biology/quast/default.nix b/pkgs/applications/science/biology/quast/default.nix index e5ee4b53089..f280f81fae8 100644 --- a/pkgs/applications/science/biology/quast/default.nix +++ b/pkgs/applications/science/biology/quast/default.nix @@ -27,7 +27,7 @@ pythonPackages.buildPythonApplication rec { --replace "/bin/bash" "${bash}/bin/bash" mkdir -p "$out/${python.sitePackages}" export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH" - ${python.pythonForBuild.interpreter} setup.py install \ + ${python.pythonOnBuildForHost.interpreter} setup.py install \ --install-lib=$out/${python.sitePackages} \ --prefix="$out" ''; diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index d6d371bf505..89fb3534c60 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -21,10 +21,10 @@ in stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.63"; + version = "2.64"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-FSs/Dbnr1shEw/W51DhUFPb61tM+0atc6wxY81EiTdM="; + sha256 = "sha256-FDL4XDHH6WYF47OsnhxpM7s7YadutiCDjcJKCF8ZlCw="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/pkgs/applications/science/chemistry/nwchem/default.nix b/pkgs/applications/science/chemistry/nwchem/default.nix index 062c61fa5c9..a7d9462a7fb 100644 --- a/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/pkgs/applications/science/chemistry/nwchem/default.nix @@ -54,13 +54,13 @@ let in stdenv.mkDerivation rec { pname = "nwchem"; - version = "7.2.1"; + version = "7.2.2"; src = fetchFromGitHub { owner = "nwchemgit"; repo = "nwchem"; rev = "v${version}-release"; - hash = "sha256-nnNTZ+c7VVGAqwOBMkBlW3rImNjs08Ne35XRkI3ssGo="; + hash = "sha256-BcYRqPaPR24OTRY0MJgBxi46HvUG4uFaY0unZmu5b9k="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 42cf5ddc951..33c77c063bf 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -8,7 +8,7 @@ , blas-ilp64 , hdf5-cpp , python3 -, texlive +, texliveMinimal , armadillo , libxc , makeWrapper @@ -78,7 +78,7 @@ stdenv.mkDerivation { perl gfortran cmake - texlive.combined.scheme-minimal + texliveMinimal makeWrapper autoPatchelfHook ]; diff --git a/pkgs/applications/science/electronics/xyce/default.nix b/pkgs/applications/science/electronics/xyce/default.nix index aee1d25a04c..663d6e025c5 100644 --- a/pkgs/applications/science/electronics/xyce/default.nix +++ b/pkgs/applications/science/electronics/xyce/default.nix @@ -16,7 +16,7 @@ , trilinos , withMPI ? false # for doc -, texlive +, texliveMedium , pandoc , enableDocs ? true # for tests @@ -81,16 +81,14 @@ stdenv.mkDerivation rec { gfortran libtool_2 ] ++ lib.optionals enableDocs [ - (texlive.combine { - inherit (texlive) - scheme-medium + (texliveMedium.withPackages (ps: with ps; [ koma-script optional framed enumitem multirow - preprint; - }) + preprint + ])) ]; buildInputs = [ diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index fe8180899c0..9717e69e9c2 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -217,7 +217,7 @@ self = stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = "https://coq.inria.fr"; license = licenses.lgpl21; branch = coq-version; maintainers = with maintainers; [ roconnor thoughtpolice vbgl Zimmi48 ]; diff --git a/pkgs/applications/science/logic/uhdm/default.nix b/pkgs/applications/science/logic/uhdm/default.nix index 7312f989cb6..ec25d58efcb 100644 --- a/pkgs/applications/science/logic/uhdm/default.nix +++ b/pkgs/applications/science/logic/uhdm/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "UHDM"; # When updating this package, also consider updating science/logic/surelog - version = "1.76"; + version = "1.77"; src = fetchFromGitHub { owner = "chipsalliance"; repo = finalAttrs.pname; rev = "v${finalAttrs.version}"; - hash = "sha256-Q/u5lvILYDT5iScES3CTPIm/B5apoOHXOQmCsZ73NlU="; + hash = "sha256-JKhpcPG4hWlcn2C+Wlx7yNIMXXurAMxLSK4xWN2akMQ="; fetchSubmodules = false; # we use all dependencies from nix }; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 9fe39c8cef8..6165cfe8bd2 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -47,7 +47,7 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: configurePhase = concatStringsSep " " ( - [ "${python.pythonForBuild.interpreter} scripts/mk_make.py --prefix=$out" ] + [ "${python.pythonOnBuildForHost.interpreter} scripts/mk_make.py --prefix=$out" ] ++ optional javaBindings "--java" ++ optional ocamlBindings "--ml" ++ optional pythonBindings "--python --pypkgdir=$out/${python.sitePackages}" diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index d3ca419c48d..814f54f3863 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng -, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texLive, tk, xz, zlib +, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata , withRecommendedPackages ? true @@ -31,7 +31,7 @@ stdenv.mkDerivation (finalAttrs: { nativeBuildInputs = [ pkg-config ]; buildInputs = [ bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses - pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu + pango pcre2 perl readline (texliveSmall.withPackages (ps: with ps; [ inconsolata helvetic ps.texinfo fancyvrb cm-super rsfs ])) xz zlib less texinfo graphviz icu bison imake which blas lapack curl tcl tk jdk tzdata ] ++ lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]; diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix index 752b05fe4fe..0dc12b6dcb0 100644 --- a/pkgs/applications/science/math/giac/default.nix +++ b/pkgs/applications/science/math/giac/default.nix @@ -1,4 +1,4 @@ -{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, lapack, blas +{ stdenv, lib, fetchurl, fetchpatch, texliveSmall, bison, flex, lapack, blas , autoreconfHook, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty , buildPackages, readline, gettext, libpng, libao, gfortran, perl , enableGUI ? false, libGL, libGLU, xorg, fltk @@ -60,7 +60,7 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ - autoreconfHook texlive.combined.scheme-small bison flex + autoreconfHook texliveSmall bison flex ]; # perl is only needed for patchShebangs fixup. diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix index 44647ce8139..2480ff3eba8 100644 --- a/pkgs/applications/science/math/pari/default.nix +++ b/pkgs/applications/science/math/pari/default.nix @@ -7,7 +7,7 @@ , libpthreadstubs , perl , readline -, tex +, texliveBasic , withThread ? true }: @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { libX11 perl readline - tex + texliveBasic ] ++ lib.optionals withThread [ libpthreadstubs ]; diff --git a/pkgs/applications/science/math/polymake/default.nix b/pkgs/applications/science/math/polymake/default.nix index 2e79ca03635..fe9210641d2 100644 --- a/pkgs/applications/science/math/polymake/default.nix +++ b/pkgs/applications/science/math/polymake/default.nix @@ -28,13 +28,13 @@ in stdenv.mkDerivation rec { pname = "polymake"; - version = "4.10"; + version = "4.11"; src = fetchurl { # "The minimal version is a packager friendly version which omits # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; - sha256 = "sha256-YDiyZtbUC76ZVe3oRtzPRBfkEU+qh+d1ZWFhzUyi+Pg="; + sha256 = "sha256-XfbwrNcAEZvQxLV2Z2KFL/vYV3ZbXcyIgC/10hCK3SM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 1f06f0d1aef..f77bd5a9224 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -17,7 +17,7 @@ # use letters instead of numbers for post-appendix chapters, and we # want it to match the upstream format because sage depends on it. , texinfo4 -, texlive +, texliveSmall , enableDocs ? !stdenv.isDarwin , enableGfanlib ? true }: @@ -86,7 +86,7 @@ stdenv.mkDerivation rec { graphviz latex2html texinfo4 - texlive.combined.scheme-small + texliveSmall ] ++ lib.optionals stdenv.isDarwin [ getconf ]; depsBuildBuild = [ buildPackages.stdenv.cc ]; diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index a03709c1437..d2172f614f6 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -110,18 +110,6 @@ stdenv.mkDerivation rec { patches = [ ./sw_vers.patch - # glibc >=2.38 already has strlcat implemented. - # merged upstream, remove on next package bump. - (fetchpatch { - url = "https://github.com/root-project/root/commit/8fb0e35446ed67c9d56639b4708c8f05459b7f84.patch"; - hash = "sha256-7EabmYanqlQsYSQsi+S9eWs1v1pY6MncopL420Y3D4w="; - }) - ] ++ lib.optionals (python.pkgs.pythonAtLeast "3.11") [ - # Fix build against Python 3.11 - (fetchpatch { - url = "https://github.com/root-project/root/commit/484deb056dacf768aba4954073b41105c431bffc.patch"; - hash = "sha256-4qur2e3SxMIPgOg4IjlvuULR2BObuP7xdvs+LmNT2/s="; - }) ]; preConfigure = '' diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 9f88fe58e3c..0ff92337566 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -4,7 +4,7 @@ stdenv.mkDerivation rec { pname = "qgroundcontrol"; - version = "4.2.8"; + version = "4.2.9"; propagatedBuildInputs = [ qtbase qtcharts qtlocation qtserialport qtsvg qtquickcontrols2 @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { owner = "mavlink"; repo = pname; rev = "v${version}"; - sha256 = "sha256-EmGtVy/cHiZ2SqOOKmt9vCUQbyT5Sl8XnkRlhn9BdvA="; + sha256 = "sha256-nzBap5ldlLLLBB1ILkOktt9FnBqbo8MALLOETiqoAzk="; fetchSubmodules = true; }; |